The US Air Force F15C Eagle – from the 48th Fighter Wing based at RAF Lakenheath in Suffolk – crashed at around 9.40am while on a routine training exercise.
In a statement on Monday evening, RAF Lakenheath said the pilot had been found and “confirmed deceased”.
“This is a tragic loss for the 48th Fighter Wing community, and our deepest condolences go out to the pilot's family and the 493rd Fighter Squadron,” the statement added.
RAF Lakenheath said the pilot's name would not be released until all next of kin notifications had been made.
RAF Lakenheath previously said search efforts by HM Coastguard had found the aircraft wreckage with recovery efforts under way.
HM Coastguard said on Monday morning that it had received reports that an aircraft went into the sea 74 miles off the coast of Flamborough Head in Yorkshire.
A Coastguard helicopter and Bridlington and Scarborough RNLI lifeboats were sent to the area.
The Coastguard also sent a Mayday broadcast, resulting in other vessels nearby heading there.
The F15C is a model of jet that has been used by the US Air Force since 1979.
RAF Lakenheath is the “largest US Air Force-operated base in England and the only US air forces in Europe F15 fighter wing”, its website said.
The 48th Fighter Wing, which has operated from the base since 1960, has more than 4,500 "active-duty military members".
Its mission statement is to "provide worldwide responsive combat air power and support".
In October 2014, an F15D fighter jet based at RAF Lakenheath crashed in fields near Spalding in Lincolnshire.
The pilot ejected safely, suffering only minor injuries, and no-one on the ground was hurt.
A US Air Force investigation found that the crash was caused by the "angle of attack" of the aircraft and "imperfections" in the assembly of the jet's nose cap.
In October 2015, US pilot Major Taj Sareen died when his F-18 Hornet jet crashed on farmland near RAF Lakenheath.
A subsequent investigation found the 34-year-old did not report problems with his aircraft before take-off.
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